Intelligent diagnosis with Chinese electronic medical records based on convolutional neural networks

Benefiting from big data, powerful computation and new algorithmic techniques, we have been witnessing the renaissance of deep learning, particularly the combination of natural language processing (NLP) and deep neural networks.

(2019) 20:62 Li et al BMC Bioinformatics https://doi.org/10.1186/s12859-019-2617-8 RESEARCH ARTICLE Open Access Intelligent diagnosis with Chinese electronic medical records based on convolutional neural networks Xiaozheng Li1 , Huazhen Wang1* , Huixin He1 , Jixiang Du1 , Jian Chen2 and Jinzhun Wu3 Abstract Background: Benefiting from big data, powerful computation and new algorithmic techniques, we have been witnessing the renaissance of deep learning, particularly the combination of natural language processing (NLP) and deep neural networks The advent of electronic medical records (EMRs) has not only changed the format of medical records but also helped users to obtain information faster However, there are many challenges regarding researching directly using Chinese EMRs, such as low quality, huge quantity, imbalance, semi-structure and non-structure, particularly the high density of the Chinese language compared with English Therefore, effective word segmentation, word representation and model architecture are the core technologies in the literature on Chinese EMRs Results: In this paper, we propose a deep learning framework to study intelligent diagnosis using Chinese EMR data, which incorporates a convolutional neural network (CNN) into an EMR classification application The novelty of this paper is reflected in the following: (1) We construct a pediatric medical dictionary based on Chinese EMRs (2) Word2vec adopted in word embedding is used to achieve the semantic description of the content of Chinese EMRs (3) A fine-tuning CNN model is constructed to feed the pediatric diagnosis with Chinese EMR data Our results on real-world pediatric Chinese EMRs demonstrate that the average accuracy and F1-score of the CNN models are up to 81%, which indicates the effectiveness of the CNN model for the classification of EMRs Particularly, a fine-tuning one-layer CNN performs best among all CNNs, recurrent neural network (RNN) (long short-term memory, gated recurrent unit) and CNN-RNN models, and the average accuracy and F1-score are both up to 83% Conclusion: The CNN framework that includes word segmentation, word embedding and model training can serve as an intelligent auxiliary diagnosis tool for pediatricians Particularly, a fine-tuning one-layer CNN performs well, which indicates that word order does not appear to have a useful effect on our Chinese EMRs Keywords: Chinese electronic medical records, Convolutional neural networks, Natural language processing Background Challenges of diagnosing using EMR data An integrated electronic medical record system is becoming an essential part of the fabric of modern healthcare, which can collect, store, display, transmit and reproduce patient information [1, 2] The current studies show that medical information provided by Electronic Medical Records (EMRs) is more complete and faster to retrieve than traditional paper records [3] Nowdays, EMRs are *Correspondence: wanghuazhen@hqu.edu.cn College of Computer Science and Technology, Huaqiao University, 361021 Xiamen, China Full list of author information is available at the end of the article becoming the main source of medical information about patients [4] The degree of health information sharing has become one of the indicators of hospital information construction in various countries Therefore, the research and application of EMRs have certain scales and experiences in the world How to use the rapidly growing EMR data to support biomedical research and clinical research is an important research content [5] Due to their semi-structured and unstructured form, the study of EMRs belongs to the specific domain of Natural Language Processing (NLP) Notably, recent years have witnessed a surge of interests in data analytics with © The Author(s) 2019 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated Li et al BMC Bioinformatics (2019) 20:62 patient EMRs using NLP Ananthakrishnan et al [6] developed a robust electronic medical record–based model for classification of inflammatory bowel disease leveraging the combination of codified data and information from clinical text notes using natural language processing Katherine et al [7] assessed whether a classification algorithm incorporating narrative EMR data (typed physician notes) more accurately classifies subjects with rheumatoid arthritis (RA) compared with an algorithm using codified EMR data alone The work by Ruben et al [8] studied a real-time electronic predictive model that identifies hospitalized heart failure (HF) patients at high risk for readmission or death, which may be valuable to clinicians and hospitals who care for these patients Although some effective NLP methods have been proposed for EMRs, lots of challenges still remain, to list a few among the most relevant ones: (1) Low-Quality Owing to the constraint of electronic medical record template, the EMRs data are similar in a large scale, especially the content of EMRs What’s more, the medical records writing is not standardized which sometimes shows inconsistency between records and doctor’s diagnosis (2) Huge-Quantity With the increasing popularity of medical information construction, EMRs data have been growing rapidly in scale and species There is a great intensive knowledge to explore in the EMRs databases (3) Imbalance Due to the wide variety of diseases (e.g., there are more than 14,000 different diagnosis codes in terms of International Classification of Diseases - 9th Version (ICD-9)) in EMRs data, the sample distribution is expected to remain rather imbalance (4) Semi-structure and non-structure The EMRs data include front sheet, progress notes, test results, medical orders, surgical records, nursing records and so on These documents include structured information, unstructured texts and graphic image information Despite the above challenges, one must address the additional challenges posed by the high density of the Chinese language compared with other languages [9] Most of words in Chinese corpus cannot be expressed independently Therefore, the word segmentation is a necessary preprocessing step, and its effect directly affects the following series NLP operations for EMRs [10] Intelligent diagnosis using EMR data In practice, a great deal of information is used to determine the disease, such as the patient’s chief complaint, current history, past history, relevant examinations However, the diagnostic accuracy not only depends on individual medical knowledge but also clinical experience Different doctors may have different diagnoses on the same patient In particular, doctors with poor skills or in remote areas have lower diagnostic accuracy Therefore, Page of 12 it’s very important and realistic to establish a intelligent dignosis model for EMRs Chen et al [11] applied machine learning methods, including support vector machine (SVM), decision forest, and a novel summed similarity measure to automatically classify the breast cancer texts on their Semantic Space models Ekong et al [12] proposed the use of fuzzy clustering algorithm for a clinical study on liver dysfunction symptoms Xu et al [13] designed and implemented a medical information text classification system based on a KNN Many researchers at home and abroad, who use EMRs for disease prediction, always focus on a particular department as well as a specific disease At present, the algorithms used by researchers mostly focus on machine learning methods, such as KNN, SVM, DT Due to the particularity of medical field and the key role of professional medical knowledge, common text classification methods often fail to achieve good classification performance and cannot meet the requirement of clinical practice [14] Benefiting from big data, powerful computation and new algorithmic techniques, we have been witnessing the renaissance of deep learning, especially the combination of natural language processing and deep neural networks Dong et al [15] presented a CNN based multiclass classification method for mining named entities with EMRs A transfer bi-directional Recurrent Neural Networks was proposed for named entity recognition (NER) in Chinese EMRs that aims to extract medical knowledge such as phrases recording diseases and treatments automatically [16] SA [17] marked the prediction of heart disease as a multi-level problem of different features or signs and constructed an IHDPS (Intelligent Heart Disease Prediction System) based on neural networks However, to the best of our knowledge, few significant models based on deep learning have been employed for the intelligent diagnosis with Chinese EMRs Rajkomar et al [18] demonstrated that deep learning methods outperformed state-of-art traditional predictive models in all cases with electronic health record (EHR) data, which is probably the first research on using deep learning methods in EHR model analysis Deep learning for natural language processing NLP is a theory-motivated range of computational techniques for the automatic analysis and representation of human language, which enables computers to perform a variety of natural language related tasks at all levels, ranging from parsing and part-of-speech (POS) tagging, to dialog systems and machine translation In recent years, Deep learning algorithms and architectures have already won numerous contests in fields such as computer vision and pattern recognition Following this trend, recent NLP research is now increasingly focusing on the use of deep learning methods [19] Li et al BMC Bioinformatics (2019) 20:62 In a deep learning with NLP model, word embedding is usually used as the first data preprocessing layer It’s because the learnt word vectors can capture general semantic and syntactical information, that word embedding produces state-of-art results on various NLP tasks [20–22] Following the success of word embedding [23, 24], CNNs turned out to be the natural choice in view of their effectiveness in computer vision and pattern recognition tasks [25–27] In 2014, Kim [28] explored using the CNNs for various sentence classification tasks, and CNNs was quickly adapted by some researchers due to its simple and effective network Poria et al [29] proposed a multi-level deep CNN to tag each word in a sentence, which coupled with a group of linguistic patterns and finally performed well in aspect detection Besides text classification, CNN models are also suitable for other NLP tasks For example, Denil et al [30] applied DCNN to map meanings of words that constitute a sentence to that of documents for summarization, which provided insights in automatic summarization of texts and the learning process In the domain of Question and Answer (QA), the work by Yih et al [31] presented a CNN architecture to measure the semantic similarity between a question and entries in a knowledge base (KB), which determined what supporting fact in the KB to look for when answering a question In the domain of Information and Retrieval (IR), Chen et al [32] proposed a dynamic multi-pooling CNN (DMCNN) strategy to overcome the loss of information for multiple-event modeling In the speech recognition, Palaz et al [33] performed extensive analysis based on a speech recognition systems with CNN framework and finally created a robust automatic speech recognition system In general, CNNs are extremely effective in mining semantic clues in contextual windows Page of 12 It is well known that pediatric patients are generally depauperate, traversing from newborns to adolescents Correspondingly, the treatment and dosage of medicine are different from those given to adult patients Thus, it is a great challenge to build a prediction model for pediatric diagnosis that is trained to “learn” expert medical knowledge to simulate the doctor’s thinking and diagnostic reasoning In this research, we propose a deep learning framework to study intelligent diagnosis using Chinese EMRs, which incorporates a convolutional neural network (CNN) into an EMR classification application This framework involves a series of operations that includes word segmentation, word embedding and model training In real pediatric Chinese EMR intelligent diagnosis applications, the proposed model has high accuracy and a high F1score, and achieves good results The novelty of this paper is reflected in the following: (1) We construct a pediatric medical dictionary based on Chinese EMRs (2) Word2vec is used as a word embedding method to achieve the semantic description of the content of Chinese EMRs (3) A fine-tuning CNN model is constructed to feed the pediatric diagnosis with Chinese EMR data Methods Proposed framework Our proposed framework is the incorporation of a CNN into the procedure of NLP with Chinese EMRs, and its schema is shown in Fig 1, which includes word segmentation, word embedding and model training First, the corpus is extracted from the Chinese EMR database Then, a medical dictionary is constructed from the original corpus, which is used as external expert knowledge in word segmentation Next, word embedding is executed Finally, Fig Schema of our proposed framework NLP technology involves a series of operations, which includes word segmentation, word embedding and model training Li et al BMC Bioinformatics (2019) 20:62 Page of 12 the CNN model is trained using a nested 5-fold crossvalidation approach The detailed design of our proposed framework is presented in the following Datasets In this paper, we explore our proposed framework for pediatric Chinese EMRs A total of 144,170 valid medical records were collected, which includes 63 types of pediatric diseases The number of samples that are “acute upper respiratory tract infection” accounts for more than 50%; hence, the sample distribution with 63 types of pediatric diseases is rather imbalanced To reduce the effect of the unbalanced dataset on the prediction model, three types of smaller datasets were constructed by downsampling the data to explore the effectiveness of our proposed framework: eight types of diseases with large sample sizes and a great difference in diseases; the top 32 types of diseases sorted by sample size; and seven types of diseases excluding "acute upper respiratory tract infection" Therefore, the text classification of 7, 8, 32 and 63 diseases were studied separately to explore the universality of the CNN model for the intelligent diagnosis of pediatric outpatients The distribution of the experimental datasets is given in Table Word segmentation Word segmentation refers to word sequences that are divided into the smallest semantically independent expressions using an algorithm [34] Generally, there are four types of mainstream methods: dictionarybased, statistics-based, comprehension-based and AIbased Dictionary-based word segmentation is widely used because of its maturity and easy implementation [35] In the process of Chinese word segmentation, particularly in specific fields such as medicine, the completeness and accuracy of domain dictionaries largely determine the performance of the word segmentation system [34] Table Distribution of datasets with respect to four types of classification applications for pediatric Chinese EMRs Number of diseases Name of diseases Number of samples Allergic rhinitis, bronchitis, acute bronchitis, 49,148 respiratory disease, bronchial asthma, no critical, diarrhea, cough variant asthma acute upper respiratory tract infection, 92,744 allergic rhinitis, bronchitis, acute bronchitis, respiratory disease, bronchialasthma, no critical, diarrhea, cough variant asthma 32 See Additional file 132,637 63 See Additional file 144,170 Boldface represents an additional disease compared with the seven-classification application For example, when “upper respiratory tract infection” is the official, full name of the disease, some Chinese physicians write “upper infection” as an informal abbreviation [36].Establishing a fast, accurate and efficient word segmentation dictionary fundamentally affects the performance of word segmentation To the best of our knowledge, there are few medical dictionaries published about pediatrics To improve the accuracy of word segmentation, a pediatric medical dictionary with a scale of 900 was established based on the collected EMR data, which was used as expert knowledge The public jieba word segmentation system was used, with a precise pattern, and the results are shown in Fig Word vector representation The core issue of NLP is how to convert a corpus into vectors; that is, each word needs to be embedded into a mathematical space to obtain the word vector expression There are two types of mainstream methods: one-hot and word2vec One-hot is an intuitive expression that represents each word as an N-dimensional vector of the same size as the vocabulary Generally, the value of the attribute that corresponds to the word is one and the values of other attributes are zero With a vocabulary scale of 5850 for the seven-classification dataset, the word “cough” is expressed as [0 0 0 0 0 0 0 0 ]5850 and the word “fever” is expressed as [0 0 0 0 0 0 0 ]5850 However, there are some defects in this method, such as the “dimensionality disaster” and semantic gap Therefore, word2vec was developed to map words to obtain K-dimensional vectors; that is, word2vec uses a low-dimensional vector to represent a large amount of potential information of a word, which overcomes the “dimensionality disaster” phenomenon Additionally, the similarity of vectors can reflect their semantic similarity [37] Word2vec is widely used in NLP, such as word clustering, POS-tagging, syntactic analysis and emotional analysis In the application of word2vec, it can be divided into the CBOW model and skip-gram model The CBOW model predicts the current word using its context word and the skip-gram model predicts its context using the current word [38] In the training procedure, the hierarchical softmax algorithm, negative sampling algorithm and sub-sampling technology were used [24, 39–43] In our study, the CBOW strategy was adopted, with the word frequency threshold set to (i.e., the least number of words that appear in the corpus), and the window size set to (i.e., the number of words in the context) When determining the dimension of word vectors, Mikolov et al [24] suggested that the classification applications of different scales should have different embedding dimensions Therefore, the four types of text classification applications in this paper have 50, 80, 100 and 100 embedding dimensions, respectively, based on their accuracies with Li et al BMC Bioinformatics (2019) 20:62 Page of 12 Fig Semantic rationality of whether to use our medical dictionary an optimal one-layer CNN The relationship between accuracy and dimension is shown in Table Consider the seven-classification application as an example Each word is embedded into 50-dimensional vector space For instance, the word “cough” is expressed as [-3.982, -0.670, -1.754, , 3.048]50 and the word "fever" is expressed as [-4.487, -5.976, -5.417, , 1.216]50 Additionally, the word vector representation using word2vec can use the cosine distance to measure the degree of semantic similarity [10] The cosine distance of words between “cough” are given in Table 3, which indicates that the smaller the cosine value, the more similar the semantics Convolutional neural networks CNNs proposed by Lecun in 1989 [44] enable automatic feature representation learning Different from the traditional feed-forward neural network, a CNN is a multilayer neural network that includes four parts, embedding layer, convolution layer, pooling layer and fully connected layer, as illustrated in Fig [45] The first layer is the input layer, which is an embedding matrix I ∈ RS* N that corresponds to the symptom text to be classified Number of rows S is the number of words in the sentence and number of columns N is the dimension of the word vector Consider the description of “cough for a week, a mild headache and runny nose" as an example The sentence is divided into "cough + a + week + a mild + headache + runny nose” when the dictionary-based word segmentation method is used Then each word is converted into a vector using word2vec, subsequently Table One-layer CNN accuracy for different dimensions with respect to four types of classification applications forming embedding matrix I as the input layer of the CNN [45] Then different filters are applied to different layers and the result is downsampled using the pooling layer CNNs realize automatic feature representation learning through multiple layers of networks, the core of which lies in the convolutional layer and pooling layer The convolution layer extracts local features, whereas the pooling layer reduces the dimension of the structured feature [46, 47] Additionally, the depth of neural networks plays a decisive role in the performance of a CNN model, and is regarded as one of the most investigated approaches used to increase its accuracy For instance, Wang et al [48] discussed the influence of the varied depth on the validation set of ILSVRC and proposed that “going deeper” is an effective and competitive approach to increase the accuracy of classification The work by Hussam et al [49] proposed a deep neural network comprised of 16 convolutional layers compressed with the Fire module adapted from the SqueezeNet model Hyperparameter setup The architecture of CNN needs fine-tuning to obtain optimal performance on specific datasets Generally, hyperparameter setup refers to the grid-search of several parameters, which include size of filter windows, number of feature Table Semantic similarity of word vectors Word Cosine distance Recurrent cough 0.6350 Quiet cough 0.6196 Bad cough 0.5433 Little cough 0.5204 0.5208 Text classification 50 (%) 80 (%) 100 (%) Dry cough classes 83.72 83.65 83.63 Nasal obstruction 0.5914 0.5434 classes 82.26 82.55 82.51 Phlegm 32 classes 73.13 73.44 73.54 Vomiting 29.48 71.2 Afternoon 23.41 Muscular stiffness 22.83 63 classes Boldface represents the best 70.39 71.06 Li et al BMC Bioinformatics (2019) 20:62 Page of 12 Fig Structure of a CNN Different from the traditional feed-forward neural network, a CNN is a multi-layer neural network, which includes four parts: embedding layer, convolution layer, pooling layer and fully connected layer maps, dropout rate, activation function, mini-batch size, and so on [28] Practically, the hyperparameter setup of CNN refers the filter windows of 7, 6, 5, and 3, the feature maps of 128, 100, 64, 50, 32 and 16, the minibatch size of 100, 95, 64, 50 and 32 In our experiments, a nested 5-fold cross-validation approach was applied on the seven-classification dataset, where the inner crossvalidation was used for the grid-search to tune the hyperparameters, and the outer cross-validation was adopted to evaluate the performance of different models mentioned in this paper As a result, we found that the one-layer CNN outperformed on the EMR-based pediatric diagnosis, whose hyperparameters included the filter windows of 7, the feature maps of 100, the dropout rate of 0.5, activation of relu and mini-batch size of 64, and the update rule of AdaMax All the experiments were conducted using Python 3.5 with Python packages Results Evaluation In this paper, we study the effectiveness of our proposed framework on real-world pediatric Chinese EMR data For each dataset, three metrics were used to evaluate the effectiveness and performance of algorithms: accuracy, precision and F1-score Precision and recall were often combined to obtain a better understanding of the performance of the classifier Their formulas for calculation are as follows: TP + TN Accuracy = (1) TP + FP + TN + FN TP Precision = (2) TP + FP TP TP + FN ∗ Precision ∗ Recall F1 − score = Precision + Recall Recall = (3) (4) where true positive (TP): scenario in text classification in which the classifier correctly classifies a positive test case into a positive class; true negative (TN): scenario in text classification in which the classifier correctly classifies a negative test case into a negative class; false positive (FP): scenario in text classification in which the classifier incorrectly classifies a negative test case into a positive class; false negative (FN): scenario in text classification in which the classifier incorrectly classifies a positive test case into a negative class Performance of the CNN models In the CNN experiments, we focused on the impact of depth on our application, that is, three different depths, depth 1, depth and depth 3, were explored to obtain an optimal solution Subsequently, the comparative results with respect to the sevenclassification application are presented in Table 4, which contains the precision, accuracy and F1-score of each fold It can be seen from Table that the accuracies of the three CNN models were all higher than 81%, and the same is true for other metrics This result indicates the effectiveness of CNN for the classification of Chinese EMRs Furthermore, one-layer CNN had the best performance among all the CNN models, which makes it the most Li et al BMC Bioinformatics (2019) 20:62 Page of 12 Table Comparative results of the CNN model with the seven-classification application Depth One-layer CNN(%) Fold\metrics Precision Accuracy F1-score Precision Two-layer CNN(%) Accuracy F1-score Precision Three-layer CNN(%) Accuracy F1-score 84.26 84.1 84.16 83.13 82.9 82.97 83.05 82.74 82.84 83.63 83.5 83.52 82.65 82.42 82.5 82.32 81.53 81.66 83.86 83.55 83.61 82.54 82.26 82.35 79.09 78.89 78.94 84.07 83.75 83.84 82.78 82.51 82.58 82.28 82.02 82.05 83.87 83.71 83.76 82.97 82.81 82.85 82.6 82.37 82.4 Average 83.94 83.72 83.78 82.81 82.58 82.65 81.87 81.51 81.58 Fig Confusion matrix of the three CNN models a normalized confusion matrix of one-layer CNN b unnormalized confusion matrix of one-layer CNN c normalized confusion matrix of two-layer CNN d normalized confusion matrix of three-layer CNN Li et al BMC Bioinformatics (2019) 20:62 Page of 12 practicable tool in pediatric diagnosis Because the experimental datasets were more than two classes and imbalanced, the confusion matrix of the three CNN models are shown in Fig 4, where Fig 4a and b show the firstfold normalized confusion matrix and its non-normalized confusion matrix for the one-layer CNN model in the outer 5-fold cross-validation, respectively The first-fold normalized confusion matrix of the two-layer CNN model and three-layer CNN model can be observed in Fig 4c and d, respectively Table Accuracies of fine-tuning the one-layer CNN model with respect to four types of classification applications CNN vs RNN models sufficient samples to train for so many different types of diseases The results of our CNN models against other methods are presented in Table The model of long short-term memory (LSTM) did not perform well The average accuracy and F1-score of the CNN models are up to 81%, which indicates the effectiveness of the CNN model for the classification of EMRs Particularly, a fine-tuning onelayer CNN performs best among all CNN, recurrent neural network (RNN) (LSTM, gated recurrent unit (GRU)) and CNN-RNN models, and the average accuracy and F1-score are both up to 83% Based on the best CNN model architecture (onelayer CNN), the other classificaion applications, i.e., eight-classification application, 32-classification application, and 63-classification application, were evaluated by the 5-fold cross-validation Table shows the model accuracies of four types of pediatric diagnosis applications It can be seen that (1) the highest accuracy was exhibited in the seven-classification application, which may have been caused by the small scale and somewhat balanced distribution of sample data; and (2) with the increase of disease types, the accuracy of the one-layer CNN model decreased The main reason was that, because of the constraint of the EMR template, the content of the EMRs were similar on a large scale Furthermore, there were not Table Results of our CNN models against other methods Model Precision(%) Accuracy(%) F1-score(%) 1-layer CNN 83.94 83.72 83.78 1-layer LSTM 43.97 46.33 38.18 1-layer GRU 82.95 82.2 82.37 2-layers CNN 82.81 82.58 82.65 2-layers LSTM 23.01 34.12 19.57 2-layers GRU 83.03 82.4 82.57 3-layers CNN 81.87 81.51 81.58 CNN-1LSTM 83.86 83.55 83.62 CNN-2LSTM 83.63 83.18 83.33 CNN-1GRU 83.42 83.02 83.13 CNN-2GRU 83.52 82.95 83.1 Boldface represents the best The number of diseases precision(%) accuracy(%) F1-score(%) classes 83.94 83.72 83.78 classes 82.35 82.55 82.27 32 classes 73.09 73.54 72.5 63 classes 70.59 71.2 69.61 Boldface represents the best Discussion Impact of the Chinese medical dictionary on word segmentation With the dictionary-based word segmentation method incorporating our pediatric medical dictionary, the corpus can be separated by "\" Fig shows the semantic rationality of whether to use our medical dictionary The second column shows the segmentation result with the absence of our medical dictionary and the third column shows the segmentation result with the adoption of our medical dictionary This shows that adopting the medical dictionary as expert knowledge accurately divided the corpus into the smallest semantic independent medical expressions, which was very helpful for the subsequent model construction Impact of various example constructions A typical medical record always contains a set of entries, such as age, gender, current status, chief complaint, present history, previous history, family history, physical examination and diagnosis An example of a medical record from the pediatric Chinese EMRs is shown in Fig Based on Fig 5, the entry of age, gender, current status, chief complaint, present history, previous history, family history and physical examination are designated as the corpus, and the initial diagnosis is designated as the label When applying a CNN model, it is necessary to convert a medical record corpus into a fixed-size matrix Considering the seven-classification application as an example, the corpus shown in Fig should be converted into a 120×50 matrix for training, and the number of words in each corpus is regularized to be 120 and the vector dimension of each word is 50 However, because the length of different medical records is different, that is, the number of words in the shortest corpus is 21 and the number of words in the longest corpus is 271, a corpus that contains records of various lengths should be truncated or filled to make the records even If the shortest medical record is chosen as the regularized length, then important information in a longer corpus may be truncated Conversely, Li et al BMC Bioinformatics (2019) 20:62 Page of 12 Fig Description of a typical pediatric Chinese EMR datum choosing the length of the longest medical record can add too many unwanted messages (fill 0) to a shorter corpus, and increase the complex of model training Therefore, we attempted to explore how three types of setup, that is, a regularized length of corpus, the truncation approach and the filling mode of the medical record, affect the performance of the CNN model For the parameter of a regularized length, we attempted 90, 100, 110, 120, 130 and 140; for the parameter of the filling mode, we considered two alternatives, that is, head-filling and tail-filling; and for the parameter of the truncation approach, we also considered two candidates, that is, head-truncation and tail-truncation Thus, a grid-search method was adopted to determine an optimal parameter setup for the aforementioned best performing CNN model (one-layer CNN) Because of the limited length of this paper, the performance of the seven-classification CNN model is Fig Impact of three types of parameter on the accuracy of the CNN model Note: “pre” refers to head-filling or head-truncation and “post” refers to tail-filling or tail-truncation For example, “pre_post” means that short text is filled by head and long text is truncated by tail Li et al BMC Bioinformatics (2019) 20:62 Page 10 of 12 Table Comparative accuracies with respect to the seven-classication application and the eight-classication application of whether to use class weights Class\metrics Name of class Sample size Seven-classication Eight-classication Without class weight With class weight Without class weight With class weight 71.09 80.1 59.68 77.85 Class1 Allergic rhinitis 1079 Class2 Respiratory disease 11980 90.37 87.92 85.28 86.3 Class3 Cough variant asthma 1418 70.31 80.74 67.12 81.45 Class4 Acute bronchitis 11990 77.5 80.00 65.56 81.78 Class5 Bronchialasthma, no critical 1550 79.23 83.56 78.82 80.77 Class6 Bronchitis 17726 82.79 73.42 66.94 51.42 Class7 Diarrhea 3405 97.91 98.7 94.9 97.06 Class8 Acute upper respiratory tract infection 43596 NA NA 92.94 84.11 Boldface represents the best illustrated in Fig The results of other classification applications were similar to those of Fig From Fig 6, we can see that the model had very robust superiority for the configuration that had the corpus length of 120, in addition to using head-filling for shorter text and tailtruncation for the longer text, which indicates that head information for longer medical records is more important than tail information, and head-filling for shorter medical records is better than tail-filling Therefore, for this optimal configuration, that is, where the regularized length of the corpus is 120, a head-filling mode and a tailtruncation approach for the medical record were adopted in our application Impact of the class weights in training In order to improve the class accuracy of small-number class caused by the unbalance distribution, different class weights serves as error-recognition penalty were introduced n_samples class_weights = (5) n_classes ∗ n_class_samples where n_samples is the number of samples, n_classes is the class number of samples and n_class_samples is the sample number of one class Table Comparative results with respect to the seven-classication application and the eight-classication application of whether to use different class weights Metrics Seven-classication Eight-classication Without class weight With class weight Without class weight With class weight Precision (%) 83.94 82.27 82.35 80.97 Accuracy (%) 83.72 80.99 82.55 78.15 F1-score (%) 83.78 81.25 82.27 78.45 Boldface represents the best Based on the best CNN model architecture (one-layer CNN), Table shows the comparative accuracies of each class with respect to the seven-classication application and the eight-classication application, and Table shows the three model evaluation indices It can be seen that: (1) the class accuracy of small number of samples has promots a lot when using class weights, at the same time, the class accuracy of large sample size has put down a lot; and (2) In a comprehensive view, it performs well in all three metrics than using the class weights Therefore, we not use class weights in our article Conclusions Considering the advantage of CNNs in local feature extraction and modeling performance, we attempted to explore a framework based on a CNN model for intelligent diagnosis with pediatric Chinese EMRs Our framework was composed of three parts: word segmentation, word embedding and model training With an expert dictionary based on collected Chinese EMR data used in word segmentation, and the word vector representation of the medical records using word2vec, we validated the effectiveness of our proposed framework on realworld EMR data A wide range of models, which included CNN models, RNN models (LSTM, GRU) and CNN-RNN hybrid architecture, were explored to determine an optimal model The comparative experimental results indicate the effectiveness of the CNN model for the classification of Chinese EMR data, which indicates that word order does not appear to have a useful effect on our Chinese EMRs Furthermore, one-layer CNN performed best among all the classification applications To conclude, the one-layer CNN model might contribute to the diagnosis of pediatric Chinese EMRs In this study, we only used EMR data and did not integrate medical images into the model Therefore, future research will focus on how to integrate multiple types of Li et al BMC Bioinformatics (2019) 20:62 medical information to improve the prediction effect for pediatric Chinese EMRs Page 11 of 12 Additional file Additional file 1: Distribution of datasets with respect to four types of classification applications for pediatric Chinese EMRs (PDF 142 kb) Abbreviations CNN: Convolutional neural network; DMCNN: Multi-pooling CNN; EHR: Electronic health record; EMRs: Electronic medicine records; GRU: Gated recurrent unit; HAL: Hyperspace analog to language; HF: Heart failure; IHDPS: Intelligent heart disease prediction system; KB: Knowledge base; LSTM: Long short-term memory; MCCNN: Multi-column CNN; NER: Named entity recognition; NLP: Natural language processing; QA: Question and answer; RNN: Recurrent neural networks Acknowledgements We thank Professor Bicheng Li for his helpful guidance during the writing of the manuscript Funding This work is partially supported by National Natural Science Foundation of China under Grant No 61673186, the Natural Science Foundation of Fujian Province in China under Grant No 2012J01274 The funders did not play any roles in the design of the study, in the collection, analysis, or interpretation of data, or in writing the manuscript Availability of data and materials The datasets generated and/or analysed during the current study are not publicly available, because all EMR data are from the First Affiliated Hospital of Xiamen University and the constraints of the privacy policies, but they are available from the corresponding author on reasonable request Authors’ contributions HZW, HXH and JZW conceived the study XZL completed experimental and wrote the initial draft of the manuscript HZW, HXH, JXD, JZW and JC gave their helpful guidance during the analysis and writing of the manuscript All authors contributed to analysing the data, writing and revising the manuscript All authors read and approved the manuscript 10 11 12 13 14 15 16 Ethics approval and consent to participate Not applicable 17 Consent for publication Not applicable 18 Competing interests The authors declare that they have no competing interests Publisher’s Note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations Author details College of Computer Science and Technology, Huaqiao University, 361021 Xiamen, China Research Department, Zhiye software, 361021 Xiamen, China Pediatric Department, The First Affiliated Hospital of Xiamen University, 361003 Xiamen, China Received: 17 March 2018 Accepted: 10 January 2019 19 20 21 22 23 References Boonstra A, Broekhuis M Barriers to the acceptance of electronic medical records by physicians from systematic review to taxonomy and interventions BMC Health Serv Res 2010;10(1):231 24 MacKinnon W, Wasserman M Integrated electronic medical record systems: Critical success factors for implementation 2009 42nd Hawaii Int Conf Syst Sci 2009;1–10 Tsai J, Bond GG A comparison of electronic records to paper records in mental health centers Int J Qual Health Care J Int Soc Qual Health Care 2008;20(2):136–43 Hu Y Research on 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